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Magnesium in PDB 3u2d: S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor

Enzymatic activity of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor

All present enzymatic activity of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor:
5.99.1.3;

Protein crystallography data

The structure of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor, PDB code: 3u2d was solved by P.A.Boriack-Sjodin, D.B.Prince, A.E.Eakin, B.A.Sherer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.77 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.487, 55.646, 51.103, 90.00, 100.38, 90.00
R / Rfree (%) 20.1 / 23.2

Other elements in 3u2d:

The structure of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor (pdb code 3u2d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor, PDB code: 3u2d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3u2d

Go back to Magnesium Binding Sites List in 3u2d
Magnesium binding site 1 out of 4 in the S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg234

b:39.2
occ:1.00
 O A:HOH282 2.0 29.5 1.0
O A:HOH380 2.1 34.2 1.0
O A:HOH379 2.1 35.4 1.0
O A:GLY208 2.1 24.4 1.0
O A:HOH327 2.3 29.0 1.0
NE2 A:HIS228 2.4 30.2 1.0
C A:GLY208 3.3 24.8 1.0
CE1 A:HIS228 3.3 30.5 1.0
CD2 A:HIS228 3.4 29.1 1.0
CA A:GLY208 3.9 25.8 1.0
O A:HOH287 4.0 35.5 1.0
O A:HOH240 4.1 27.2 1.0
O A:HOH329 4.2 33.2 1.0
N A:ILE209 4.4 23.9 1.0
O A:ASN65 4.4 22.4 1.0
ND1 A:HIS228 4.4 30.3 1.0
CB A:ASN65 4.4 23.8 1.0
CG A:HIS228 4.5 28.0 1.0
N A:GLN210 4.5 22.8 1.0
OE1 A:GLU230 4.6 31.1 0.0
CA A:ILE209 4.6 23.0 1.0
C A:ILE209 4.8 23.0 1.0
CG A:ASN65 4.9 24.8 1.0

Magnesium binding site 2 out of 4 in 3u2d

Go back to Magnesium Binding Sites List in 3u2d
Magnesium binding site 2 out of 4 in the S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg235

b:44.4
occ:1.00
 O A:HOH283 2.4 27.2 1.0
O B:HOH247 2.7 22.3 1.0
OE1 A:GLU164 2.7 28.6 1.0
O B:HOH290 2.9 25.3 1.0
O A:HOH337 3.0 33.4 1.0
O B:LEU60 3.2 23.1 1.0
CD A:GLU164 3.4 27.0 1.0
OE2 A:GLU164 3.5 28.2 1.0
C B:LEU60 3.9 22.5 1.0
CB B:LEU60 4.0 22.7 1.0
O B:HOH295 4.4 15.8 1.0
CA B:LEU60 4.5 22.4 1.0
O A:HOH347 4.5 21.1 1.0
N B:ALA61 4.6 21.9 1.0
O B:HOH341 4.7 39.6 1.0
OG1 A:THR147 4.7 21.9 1.0
CG A:GLU164 4.8 24.9 1.0
CA B:ALA61 4.9 22.6 1.0
CD2 B:LEU60 4.9 24.6 1.0

Magnesium binding site 3 out of 4 in 3u2d

Go back to Magnesium Binding Sites List in 3u2d
Magnesium binding site 3 out of 4 in the S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:62.2
occ:1.00
 O B:HOH308 2.1 34.7 1.0
O B:HOH383 2.1 42.7 1.0
O B:HOH318 2.3 27.7 1.0
OD1 B:ASN54 2.5 29.4 1.0
O B:HOH351 2.6 36.5 1.0
CG B:ASN54 3.4 25.0 1.0
ND2 B:ASN54 3.7 26.5 1.0
O B:HOH250 4.1 34.6 1.0
O B:HOH384 4.3 32.9 1.0
OE1 B:GLU50 4.3 33.2 1.0
O B:HOH267 4.4 27.5 1.0
O B:GLU50 4.4 23.9 1.0
OD2 B:ASP53 4.5 26.3 0.5
CB B:ASN54 4.7 22.6 1.0
O B:HOH248 4.8 37.7 1.0
O B:HOH329 4.8 32.1 1.0
CA B:ASN54 4.9 22.4 1.0
N B:ASN54 4.9 22.2 1.0

Magnesium binding site 4 out of 4 in 3u2d

Go back to Magnesium Binding Sites List in 3u2d
Magnesium binding site 4 out of 4 in the S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Aureus Gyrb Atpase Domain in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg234

b:49.9
occ:1.00
 O B:HOH294 2.0 18.2 1.0
O B:HOH313 2.1 30.4 1.0
O B:GLY208 2.1 25.5 1.0
O B:HOH333 2.4 24.8 1.0
NE2 B:HIS228 2.7 32.0 1.0
C B:GLY208 3.3 24.9 1.0
CE1 B:HIS228 3.3 32.1 1.0
CD2 B:HIS228 3.8 30.5 1.0
CA B:GLY208 3.9 26.1 1.0
O B:HOH254 4.0 23.9 1.0
O B:ASN65 4.3 22.3 1.0
N B:ILE209 4.3 23.9 1.0
CB B:ASN65 4.5 23.5 1.0
ND1 B:HIS228 4.5 30.4 1.0
CA B:ILE209 4.6 22.8 1.0
N B:GLN210 4.7 21.8 1.0
CG B:HIS228 4.8 28.7 1.0
CG B:ASN65 4.8 24.1 1.0
C B:ILE209 4.9 22.4 1.0

Reference:

A.E.Eakin, O.Green, N.Hales, G.K.Walkup, S.Bist, A.Singh, G.Mullen, J.Bryant, K.Embrey, N.Gao, A.Breeze, D.Timms, B.Andrews, M.Uria-Nickelsen, J.Demeritt, J.T.Loch, K.Hull, A.Blodgett, R.N.Illingworth, B.Prince, P.A.Boriack-Sjodin, S.Hauck, L.J.Macpherson, H.Ni, B.Sherer. Pyrrolamide Dna Gyrase Inhibitors: Fragment-Based Nuclear Magnetic Resonance Screening to Identify Antibacterial Agents. Antimicrob.Agents Chemother. V. 56 1240 2012.
ISSN: ISSN 0066-4804
PubMed: 22183167
DOI: 10.1128/AAC.05485-11
Page generated: Thu Aug 15 12:18:58 2024

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